# 27 UbiQuinone conformer setting
# Zhenyu Zhu 12/12/03

# Atoms deleted by Beicer C. Tapia (2/15/07)
# Ubiquinone file - deleted atoms
# Only ring, oxygens and methyl

# 27 UbiQuinone conformer setting
# Zhenyu Zhu 12/12/03
# 1.Basic Conformer Information: name, pka, em, rxn.
# 23456789A123456789B123456789C
# corrected rxn to kcal/mol 1/10/04 mg

# Modified by Beicer C. Tapia 
# Only 3 states, Ub101, Ub1-1, Ub1H2
# 12/22/08
# Protein Cytochrome bc1 complex
# PDB - 2IBZ

# NOTE - THIS FILE DOES CONTAIN THE TAIL OF UBIQUINONE


CONFLIST Ub1        Ub1BK Ub101 Ub1-1 Ub1H2 

NATOM    Ub1BK      76
NATOM    Ub101      25
NATOM    Ub1-1      25
NATOM    Ub1H2      27

IATOM    Ub1BK  C8  0
IATOM    Ub1BK  C9  1
IATOM    Ub1BK  C10 2
IATOM    Ub1BK  C11 3
IATOM    Ub1BK  C12 4
IATOM    Ub1BK  C13 5
IATOM    Ub1BK  C14 6
IATOM    Ub1BK  C15 7
IATOM    Ub1BK  C16 8
IATOM    Ub1BK  C17 9
IATOM    Ub1BK  C18 10
IATOM    Ub1BK  C19 11
IATOM    Ub1BK  C20 12
IATOM    Ub1BK  C21 13
IATOM    Ub1BK  C22 14
IATOM    Ub1BK  C23 15
IATOM    Ub1BK  C24 16
IATOM    Ub1BK  C25 17
IATOM    Ub1BK  C26 18
IATOM    Ub1BK  C27 19
IATOM    Ub1BK  C28 20
IATOM    Ub1BK  C29 21
IATOM    Ub1BK  C30 22
IATOM    Ub1BK  C31 23
IATOM    Ub1BK  C32 24
IATOM    Ub1BK  C33 25
IATOM    Ub1BK  C34 26
IATOM    Ub1BK  C35 27
IATOM    Ub1BK  C36 28
IATOM    Ub1BK  H8  29
IATOM    Ub1BK 1H10 30
IATOM    Ub1BK 2H10 31
IATOM    Ub1BK 3H10 32
IATOM    Ub1BK 1H11 33
IATOM    Ub1BK 2H11 34
IATOM    Ub1BK 1H12 35
IATOM    Ub1BK 2H12 36
IATOM    Ub1BK  H13 37
IATOM    Ub1BK 1H15 38
IATOM    Ub1BK 2H15 39
IATOM    Ub1BK 3H15 40
IATOM    Ub1BK 1H16 41
IATOM    Ub1BK 2H16 42
IATOM    Ub1BK 1H17 43
IATOM    Ub1BK 2H17 44
IATOM    Ub1BK  H18 45
IATOM    Ub1BK 1H20 46
IATOM    Ub1BK 2H20 47
IATOM    Ub1BK 3H20 48
IATOM    Ub1BK 1H21 49
IATOM    Ub1BK 2H21 50
IATOM    Ub1BK 1H22 51
IATOM    Ub1BK 2H22 52
IATOM    Ub1BK  H23 53
IATOM    Ub1BK 1H25 54
IATOM    Ub1BK 2H25 55
IATOM    Ub1BK 3H25 56
IATOM    Ub1BK 1H26 57
IATOM    Ub1BK 2H26 58
IATOM    Ub1BK 1H27 59
IATOM    Ub1BK 2H27 60
IATOM    Ub1BK  H28 61
IATOM    Ub1BK 1H30 62
IATOM    Ub1BK 2H30 63
IATOM    Ub1BK 3H30 64
IATOM    Ub1BK 1H31 65
IATOM    Ub1BK 2H31 66
IATOM    Ub1BK 1H32 67
IATOM    Ub1BK 2H32 68
IATOM    Ub1BK  H33 69
IATOM    Ub1BK 1H35 70
IATOM    Ub1BK 2H35 71
IATOM    Ub1BK 3H35 72
IATOM    Ub1BK 1H36 73
IATOM    Ub1BK 2H36 74
IATOM    Ub1BK 3H36 75

IATOM    Ub101  C1  0
IATOM    Ub101  C2  1
IATOM    Ub101  C3  2
IATOM    Ub101  C4  3
IATOM    Ub101  C5  4
IATOM    Ub101  C6  5
IATOM    Ub101  C1M 6
IATOM    Ub101  C3M 7
IATOM    Ub101  C4M 8
IATOM    Ub101  C7  9
IATOM    Ub101 1H1M 10
IATOM    Ub101 2H1M 11
IATOM    Ub101 3H1M 12
IATOM    Ub101 1H3M 13
IATOM    Ub101 2H3M 14
IATOM    Ub101 3H3M 15
IATOM    Ub101 1H4M 16
IATOM    Ub101 2H4M 17
IATOM    Ub101 3H4M 18
IATOM    Ub101 1H7  19
IATOM    Ub101 2H7  20
IATOM    Ub101  O2  21
IATOM    Ub101  O5  22
IATOM    Ub101  O3  23
IATOM    Ub101  O4  24

IATOM    Ub1-1  C1  0
IATOM    Ub1-1  C2  1
IATOM    Ub1-1  C3  2
IATOM    Ub1-1  C4  3
IATOM    Ub1-1  C5  4
IATOM    Ub1-1  C6  5
IATOM    Ub1-1  C1M 6
IATOM    Ub1-1  C3M 7
IATOM    Ub1-1  C4M 8
IATOM    Ub1-1  C7  9
IATOM    Ub1-1 1H1M 10
IATOM    Ub1-1 2H1M 11
IATOM    Ub1-1 3H1M 12
IATOM    Ub1-1 1H3M 13
IATOM    Ub1-1 2H3M 14
IATOM    Ub1-1 3H3M 15
IATOM    Ub1-1 1H4M 16
IATOM    Ub1-1 2H4M 17
IATOM    Ub1-1 3H4M 18
IATOM    Ub1-1 1H7  19
IATOM    Ub1-1 2H7  20
IATOM    Ub1-1  O2  21
IATOM    Ub1-1  O5  22
IATOM    Ub1-1  O3  23
IATOM    Ub1-1  O4  24

IATOM    Ub1H2  C1  0
IATOM    Ub1H2  C2  1
IATOM    Ub1H2  C3  2
IATOM    Ub1H2  C4  3
IATOM    Ub1H2  C5  4
IATOM    Ub1H2  C6  5
IATOM    Ub1H2  C1M 6
IATOM    Ub1H2  C3M 7
IATOM    Ub1H2  C4M 8
IATOM    Ub1H2  C7  9
IATOM    Ub1H2 1H1M 10
IATOM    Ub1H2 2H1M 11
IATOM    Ub1H2 3H1M 12
IATOM    Ub1H2 1H3M 13
IATOM    Ub1H2 2H3M 14
IATOM    Ub1H2 3H3M 15
IATOM    Ub1H2 1H4M 16
IATOM    Ub1H2 2H4M 17
IATOM    Ub1H2 3H4M 18
IATOM    Ub1H2 1H7  19
IATOM    Ub1H2 2H7  20
IATOM    Ub1H2  O3  21
IATOM    Ub1H2  O4  22
IATOM    Ub1H2  O2  23
IATOM    Ub1H2  O5  24
IATOM    Ub1H2  HO2 25
IATOM    Ub1H2  HO5 26

ATOMNAME Ub1BK    0  C8 
ATOMNAME Ub1BK    1  C9 
ATOMNAME Ub1BK    2  C10
ATOMNAME Ub1BK    3  C11
ATOMNAME Ub1BK    4  C12
ATOMNAME Ub1BK    5  C13
ATOMNAME Ub1BK    6  C14
ATOMNAME Ub1BK    7  C15
ATOMNAME Ub1BK    8  C16
ATOMNAME Ub1BK    9  C17
ATOMNAME Ub1BK   10  C18
ATOMNAME Ub1BK   11  C19
ATOMNAME Ub1BK   12  C20
ATOMNAME Ub1BK   13  C21
ATOMNAME Ub1BK   14  C22
ATOMNAME Ub1BK   15  C23
ATOMNAME Ub1BK   16  C24
ATOMNAME Ub1BK   17  C25
ATOMNAME Ub1BK   18  C26
ATOMNAME Ub1BK   19  C27
ATOMNAME Ub1BK   20  C28
ATOMNAME Ub1BK   21  C29
ATOMNAME Ub1BK   22  C30
ATOMNAME Ub1BK   23  C31
ATOMNAME Ub1BK   24  C32
ATOMNAME Ub1BK   25  C33
ATOMNAME Ub1BK   26  C34
ATOMNAME Ub1BK   27  C35
ATOMNAME Ub1BK   28  C36
ATOMNAME Ub1BK   29  H8 
ATOMNAME Ub1BK   30 1H10
ATOMNAME Ub1BK   31 2H10
ATOMNAME Ub1BK   32 3H10
ATOMNAME Ub1BK   33 1H11
ATOMNAME Ub1BK   34 2H11
ATOMNAME Ub1BK   35 1H12
ATOMNAME Ub1BK   36 2H12
ATOMNAME Ub1BK   37  H13
ATOMNAME Ub1BK   38 1H15
ATOMNAME Ub1BK   39 2H15
ATOMNAME Ub1BK   40 3H15
ATOMNAME Ub1BK   41 1H16
ATOMNAME Ub1BK   42 2H16
ATOMNAME Ub1BK   43 1H17
ATOMNAME Ub1BK   44 2H17
ATOMNAME Ub1BK   45  H18
ATOMNAME Ub1BK   46 1H20
ATOMNAME Ub1BK   47 2H20
ATOMNAME Ub1BK   48 3H20
ATOMNAME Ub1BK   49 1H21
ATOMNAME Ub1BK   50 2H21
ATOMNAME Ub1BK   51 1H22
ATOMNAME Ub1BK   52 2H22
ATOMNAME Ub1BK   53  H23
ATOMNAME Ub1BK   54 1H25
ATOMNAME Ub1BK   55 2H25
ATOMNAME Ub1BK   56 3H25
ATOMNAME Ub1BK   57 1H26
ATOMNAME Ub1BK   58 2H26
ATOMNAME Ub1BK   59 1H27
ATOMNAME Ub1BK   60 2H27
ATOMNAME Ub1BK   61  H28
ATOMNAME Ub1BK   62 1H30
ATOMNAME Ub1BK   63 2H30
ATOMNAME Ub1BK   64 3H30
ATOMNAME Ub1BK   65 1H31
ATOMNAME Ub1BK   66 2H31
ATOMNAME Ub1BK   67 1H32
ATOMNAME Ub1BK   68 2H32
ATOMNAME Ub1BK   69  H33
ATOMNAME Ub1BK   70 1H35
ATOMNAME Ub1BK   71 2H35
ATOMNAME Ub1BK   72 3H35
ATOMNAME Ub1BK   73 1H36
ATOMNAME Ub1BK   74 2H36
ATOMNAME Ub1BK   75 3H36

ATOMNAME Ub101    0  C1 
ATOMNAME Ub101    1  C2 
ATOMNAME Ub101    2  C3 
ATOMNAME Ub101    3  C4 
ATOMNAME Ub101    4  C5 
ATOMNAME Ub101    5  C6 
ATOMNAME Ub101    6  C1M
ATOMNAME Ub101    7  C3M
ATOMNAME Ub101    8  C4M
ATOMNAME Ub101    9  C7 
ATOMNAME Ub101   10 1H1M
ATOMNAME Ub101   11 2H1M
ATOMNAME Ub101   12 3H1M
ATOMNAME Ub101   13 1H3M
ATOMNAME Ub101   14 2H3M
ATOMNAME Ub101   15 3H3M
ATOMNAME Ub101   16 1H4M
ATOMNAME Ub101   17 2H4M
ATOMNAME Ub101   18 3H4M
ATOMNAME Ub101   19 1H7 
ATOMNAME Ub101   20 2H7 
ATOMNAME Ub101   21  O2 
ATOMNAME Ub101   22  O5 
ATOMNAME Ub101   23  O3 
ATOMNAME Ub101   24  O4 

ATOMNAME Ub1-1    0  C1 
ATOMNAME Ub1-1    1  C2 
ATOMNAME Ub1-1    2  C3 
ATOMNAME Ub1-1    3  C4 
ATOMNAME Ub1-1    4  C5 
ATOMNAME Ub1-1    5  C6 
ATOMNAME Ub1-1    6  C1M
ATOMNAME Ub1-1    7  C3M
ATOMNAME Ub1-1    8  C4M
ATOMNAME Ub1-1    9  C7 
ATOMNAME Ub1-1   10 1H1M
ATOMNAME Ub1-1   11 2H1M
ATOMNAME Ub1-1   12 3H1M
ATOMNAME Ub1-1   13 1H3M
ATOMNAME Ub1-1   14 2H3M
ATOMNAME Ub1-1   15 3H3M
ATOMNAME Ub1-1   16 1H4M
ATOMNAME Ub1-1   17 2H4M
ATOMNAME Ub1-1   18 3H4M
ATOMNAME Ub1-1   19 1H7 
ATOMNAME Ub1-1   20 2H7 
ATOMNAME Ub1-1   21  O2 
ATOMNAME Ub1-1   22  O5 
ATOMNAME Ub1-1   23  O3 
ATOMNAME Ub1-1   24  O4 

ATOMNAME Ub1H2    0  C1 
ATOMNAME Ub1H2    1  C2 
ATOMNAME Ub1H2    2  C3 
ATOMNAME Ub1H2    3  C4 
ATOMNAME Ub1H2    4  C5 
ATOMNAME Ub1H2    5  C6 
ATOMNAME Ub1H2    6  C1M
ATOMNAME Ub1H2    7  C3M
ATOMNAME Ub1H2    8  C4M
ATOMNAME Ub1H2    9  C7 
ATOMNAME Ub1H2   10 1H1M
ATOMNAME Ub1H2   11 2H1M
ATOMNAME Ub1H2   12 3H1M
ATOMNAME Ub1H2   13 1H3M
ATOMNAME Ub1H2   14 2H3M
ATOMNAME Ub1H2   15 3H3M
ATOMNAME Ub1H2   16 1H4M
ATOMNAME Ub1H2   17 2H4M
ATOMNAME Ub1H2   18 3H4M
ATOMNAME Ub1H2   19 1H7 
ATOMNAME Ub1H2   20 2H7 
ATOMNAME Ub1H2   21  O3 
ATOMNAME Ub1H2   22  O4 
ATOMNAME Ub1H2   23  O2 
ATOMNAME Ub1H2   24  O5 
ATOMNAME Ub1H2   25  HO2
ATOMNAME Ub1H2   26  HO5

#1.Basic Conformer Information: name, pka, em, rxn.
#23456789A123456789B123456789C

PROTON   Ub101      0
PROTON   Ub1-1      0
PROTON   Ub1H2      2

PKA      Ub101      0.0
PKA      Ub1-1      0.0
PKA      Ub1H2      3.98

ELECTRON Ub101      0
ELECTRON Ub1-1      1
ELECTRON Ub1H2      2

EM       Ub101      0.0
EM       Ub1-1      -145
EM       Ub1H2      294.

RXN      Ub101      -3.56      
RXN      Ub1-1      -18.10     
RXN      Ub1H2      -4.07      

#2.Structure Connectivity
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#ONNECT   conf atom  orbital  ires conn ires conn ires conn ires conn
#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
# Ubiquinone backbone
CONNECT  Ub1BK  C8        sp2    0  C7     0  C9     0  H8  
CONNECT  Ub1BK  C9        sp2    0  C8     0  C10    0  C11 
CONNECT  Ub1BK  C10       sp3    0  C9     0 1H10    0 2H10    0 3H10
CONNECT  Ub1BK  C11       sp3    0  C9     0  C12    0 1H11    0 2H11
CONNECT  Ub1BK  C12       sp3    0  C11    0  C13    0 1H12    0 2H12
CONNECT  Ub1BK  C13       sp2    0  C12    0  C14    0  H13 
CONNECT  Ub1BK  C14       sp2    0  C13    0  C15    0  C16 
CONNECT  Ub1BK  C15       sp3    0  C14    0 1H15    0 2H15    0 3H15
CONNECT  Ub1BK  C16       sp3    0  C14    0  C17    0 1H16    0 2H16
CONNECT  Ub1BK  C17       sp3    0  C16    0  C18    0 1H17    0 2H17
CONNECT  Ub1BK  C18       sp2    0  C17    0  C19    0  H18 
CONNECT  Ub1BK  C19       sp2    0  C18    0  C20    0  C21 
CONNECT  Ub1BK  C20       sp3    0  C19    0 1H20    0 2H20    0 3H20
CONNECT  Ub1BK  C21       sp3    0  C19    0  C22    0 1H21    0 2H21
CONNECT  Ub1BK  C22       sp3    0  C21    0  C23    0 1H22    0 2H22
CONNECT  Ub1BK  C23       sp2    0  C22    0  C24    0  H23 
CONNECT  Ub1BK  C24       sp2    0  C23    0  C25    0  C26 
CONNECT  Ub1BK  C25       sp3    0  C24    0 1H25    0 2H25    0 3H25
CONNECT  Ub1BK  C26       sp3    0  C24    0  C27    0 1H26    0 2H26
CONNECT  Ub1BK  C27       sp3    0  C26    0  C28    0 1H27    0 2H27
CONNECT  Ub1BK  C28       sp2    0  C27    0  C29    0  H28 
CONNECT  Ub1BK  C29       sp2    0  C28    0  C30    0  C31 
CONNECT  Ub1BK  C30       sp3    0  C29    0 1H30    0 2H30    0 3H30
CONNECT  Ub1BK  C31       sp3    0  C29    0  C32    0 1H31    0 2H31
CONNECT  Ub1BK  C32       sp3    0  C31    0  C33    0 1H32    0 2H32
CONNECT  Ub1BK  C33       sp2    0  C32    0  C34    0  H33 
CONNECT  Ub1BK  C34       sp2    0  C33    0  C35    0  C36 
CONNECT  Ub1BK  C35       sp3    0  C34    0 1H35    0 2H35    0 3H35
CONNECT  Ub1BK  C36       sp3    0  C34    0 1H36    0 2H36    0 3H36
CONNECT  Ub1BK  H8          s    0  C8  
CONNECT  Ub1BK 1H10         s    0  C10 
CONNECT  Ub1BK 2H10         s    0  C10 
CONNECT  Ub1BK 3H10         s    0  C10 
CONNECT  Ub1BK 1H11         s    0  C11 
CONNECT  Ub1BK 2H11         s    0  C11 
CONNECT  Ub1BK 1H12         s    0  C12 
CONNECT  Ub1BK 2H12         s    0  C12 
CONNECT  Ub1BK  H13         s    0  C13 
CONNECT  Ub1BK 1H15         s    0  C15 
CONNECT  Ub1BK 2H15         s    0  C15 
CONNECT  Ub1BK 3H15         s    0  C15 
CONNECT  Ub1BK 1H16         s    0  C16 
CONNECT  Ub1BK 2H16         s    0  C16 
CONNECT  Ub1BK 1H17         s    0  C17 
CONNECT  Ub1BK 2H17         s    0  C17 
CONNECT  Ub1BK  H18         s    0  C18 
CONNECT  Ub1BK 1H20         s    0  C20 
CONNECT  Ub1BK 2H20         s    0  C20 
CONNECT  Ub1BK 3H20         s    0  C20 
CONNECT  Ub1BK 1H21         s    0  C21 
CONNECT  Ub1BK 2H21         s    0  C21 
CONNECT  Ub1BK 1H22         s    0  C22 
CONNECT  Ub1BK 2H22         s    0  C22 
CONNECT  Ub1BK  H23         s    0  C23 
CONNECT  Ub1BK 1H25         s    0  C25 
CONNECT  Ub1BK 2H25         s    0  C25 
CONNECT  Ub1BK 3H25         s    0  C25 
CONNECT  Ub1BK 1H26         s    0  C26 
CONNECT  Ub1BK 2H26         s    0  C26 
CONNECT  Ub1BK 1H27         s    0  C27 
CONNECT  Ub1BK 2H27         s    0  C27 
CONNECT  Ub1BK  H28         s    0  C28 
CONNECT  Ub1BK 1H30         s    0  C30 
CONNECT  Ub1BK 2H30         s    0  C30 
CONNECT  Ub1BK 3H30         s    0  C30 
CONNECT  Ub1BK 1H31         s    0  C31 
CONNECT  Ub1BK 2H31         s    0  C31 
CONNECT  Ub1BK 1H32         s    0  C32 
CONNECT  Ub1BK 2H32         s    0  C32 
CONNECT  Ub1BK  H33         s    0  C33 
CONNECT  Ub1BK 1H35         s    0  C35 
CONNECT  Ub1BK 2H35         s    0  C35 
CONNECT  Ub1BK 3H35         s    0  C35 
CONNECT  Ub1BK 1H36         s    0  C36 
CONNECT  Ub1BK 2H36         s    0  C36 
CONNECT  Ub1BK 3H36         s    0  C36 

#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
#Ub101----neutral quinone //proton #:0; electron #:0
CONNECT  Ub101  C1  sp2       0     C2  0     C6  0     C1M 
CONNECT  Ub101  C2  sp2       0     C1  0     C3  0     O2  
CONNECT  Ub101  C3  sp2       0     C2  0     C4  0     O3  
CONNECT  Ub101  C4  sp2       0     C3  0     C5  0     O4  
CONNECT  Ub101  C5  sp2       0     C4  0     C6  0     O5  
CONNECT  Ub101  C6  sp2       0     C5  0     C1  0     C7
CONNECT  Ub101  C1M sp3       0     C1  0    1H1M 0    2H1M 0    3H1M 
CONNECT  Ub101  C3M sp3       0     C3  0    1H3M 0    2H3M 0    3H3M 
CONNECT  Ub101  C4M sp3       0     C4  0    1H4M 0    2H4M 0    3H4M 
CONNECT  Ub101  C7  sp3       0     C6  0    1H7  0    2H7      
CONNECT  Ub101 1H1M s         0     C1M           
CONNECT  Ub101 2H1M s         0     C1M           
CONNECT  Ub101 3H1M s         0     C1M           
CONNECT  Ub101 1H3M s         0     C3M           
CONNECT  Ub101 2H3M s         0     C3M           
CONNECT  Ub101 3H3M s         0     C3M           
CONNECT  Ub101 1H4M s         0     C4M           
CONNECT  Ub101 2H4M s         0     C4M           
CONNECT  Ub101 3H4M s         0     C4M           
CONNECT  Ub101 1H7  s         0     C7  
CONNECT  Ub101 2H7  s         0     C7
CONNECT  Ub101  O2  sp2       0     C2 
CONNECT  Ub101  O5  sp2       0     C5
CONNECT  Ub101  O3  sp2       0     C3  0    C3M
CONNECT  Ub101  O4  sp2       0     C4  0    C4M

#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
#Ub1-1----semiquone quinone //proton #:0; electron #:-1
CONNECT  Ub1-1  C1  sp2       0     C2  0     C6  0     C1M 
CONNECT  Ub1-1  C2  sp2       0     C1  0     C3  0     O2  
CONNECT  Ub1-1  C3  sp2       0     C2  0     C4  0     O3  
CONNECT  Ub1-1  C4  sp2       0     C3  0     C5  0     O4  
CONNECT  Ub1-1  C5  sp2       0     C4  0     C6  0     O5  
CONNECT  Ub1-1  C6  sp2       0     C5  0     C1  0     C7  
CONNECT  Ub1-1  C1M sp3       0     C1  0    1H1M 0    2H1M 0    3H1M 
CONNECT  Ub1-1  C3M sp3       0     C3  0    1H3M 0    2H3M 0    3H3M 
CONNECT  Ub1-1  C4M sp3       0     C4  0    1H4M 0    2H4M 0    3H4M 
CONNECT  Ub1-1  C7  sp3       0     C6  0    1H7  0    2H7      
CONNECT  Ub1-1 1H1M s         0     C1M           
CONNECT  Ub1-1 2H1M s         0     C1M           
CONNECT  Ub1-1 3H1M s         0     C1M           
CONNECT  Ub1-1 1H3M s         0     C3M           
CONNECT  Ub1-1 2H3M s         0     C3M           
CONNECT  Ub1-1 3H3M s         0     C3M           
CONNECT  Ub1-1 1H4M s         0     C4M           
CONNECT  Ub1-1 2H4M s         0     C4M           
CONNECT  Ub1-1 3H4M s         0     C4M           
CONNECT  Ub1-1 1H7  s         0     C7  
CONNECT  Ub1-1 2H7  s         0     C7
CONNECT  Ub1-1  O2  sp2       0     C2
CONNECT  Ub1-1  O5  sp2       0     C5
CONNECT  Ub1-1  O3  sp2       0     C3  0     C3M
CONNECT  Ub1-1  O4  sp2       0     C4  0     C4M

#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|----|----|
#Ub1H2----//proton #:2; electron #:-2
CONNECT  Ub1H2  C1  sp2       0     C2  0     C6  0     C1M 
CONNECT  Ub1H2  C2  sp2       0     C1  0     C3  0     O2  
CONNECT  Ub1H2  C3  sp2       0     C2  0     C4  0     O3  
CONNECT  Ub1H2  C4  sp2       0     C3  0     C5  0     O4  
CONNECT  Ub1H2  C5  sp2       0     C4  0     C6  0     O5  
CONNECT  Ub1H2  C6  sp2       0     C5  0     C1  0     C7  
CONNECT  Ub1H2  C1M sp3       0     C1  0    1H1M 0    2H1M 0    3H1M 
CONNECT  Ub1H2  C3M sp3       0     C3  0    1H3M 0    2H3M 0    3H3M 
CONNECT  Ub1H2  C4M sp3       0     C4  0    1H4M 0    2H4M 0    3H4M 
CONNECT  Ub1H2  C7  sp3       0     C6  0    1H7  0    2H7       
CONNECT  Ub1H2 1H1M s         0     C1M           
CONNECT  Ub1H2 2H1M s         0     C1M           
CONNECT  Ub1H2 3H1M s         0     C1M           
CONNECT  Ub1H2 1H3M s         0     C3M           
CONNECT  Ub1H2 2H3M s         0     C3M           
CONNECT  Ub1H2 3H3M s         0     C3M           
CONNECT  Ub1H2 1H4M s         0     C4M           
CONNECT  Ub1H2 2H4M s         0     C4M           
CONNECT  Ub1H2 3H4M s         0     C4M           
CONNECT  Ub1H2 1H7  s         0     C7  
CONNECT  Ub1H2 2H7  s         0     C7  
CONNECT  Ub1H2  O3  sp2       0     C3  0     C3M
CONNECT  Ub1H2  O4  sp2       0     C4  0     C4M
CONNECT  Ub1H2  O2  sp2       0     C2  0     HO2 
CONNECT  Ub1H2  O5  sp2       0     C5  0     HO5 
CONNECT  Ub1H2  HO2 s         0     O2 
CONNECT  Ub1H2  HO5 s         0     O5 

#3.Atom Parameters: Partial Charges and Radii
#23456789A123456789B123456789C
# Backbone
RADIUS   Ub1    C8  1.70
RADIUS   Ub1    C9  1.70
RADIUS   Ub1    C10 1.70
RADIUS   Ub1    C11 1.70
RADIUS   Ub1    C12 1.70
RADIUS   Ub1    C13 1.70
RADIUS   Ub1    C14 1.70
RADIUS   Ub1    C15 1.70
RADIUS   Ub1    C16 1.70
RADIUS   Ub1    C17 1.70
RADIUS   Ub1    C18 1.70
RADIUS   Ub1    C19 1.70
RADIUS   Ub1    C20 1.70
RADIUS   Ub1    C21 1.70
RADIUS   Ub1    C22 1.70
RADIUS   Ub1    C23 1.70
RADIUS   Ub1    C24 1.70
RADIUS   Ub1    C25 1.70
RADIUS   Ub1    C26 1.70
RADIUS   Ub1    C27 1.70
RADIUS   Ub1    C28 1.70
RADIUS   Ub1    C29 1.70
RADIUS   Ub1    C30 1.70
RADIUS   Ub1    C31 1.70
RADIUS   Ub1    C32 1.70
RADIUS   Ub1    C33 1.70
RADIUS   Ub1    C34 1.70
RADIUS   Ub1    C35 1.70
RADIUS   Ub1    C36 1.70
RADIUS   Ub1    H8  1.00
RADIUS   Ub1    H10 1.00
RADIUS   Ub1    H10 1.00
RADIUS   Ub1    H10 1.00
RADIUS   Ub1    H11 1.00
RADIUS   Ub1    H11 1.00
RADIUS   Ub1    H12 1.00
RADIUS   Ub1    H12 1.00
RADIUS   Ub1    H13 1.00
RADIUS   Ub1    H15 1.00
RADIUS   Ub1    H15 1.00
RADIUS   Ub1    H15 1.00
RADIUS   Ub1    H16 1.00
RADIUS   Ub1    H16 1.00
RADIUS   Ub1    H17 1.00
RADIUS   Ub1    H17 1.00
RADIUS   Ub1    H18 1.00
RADIUS   Ub1    H20 1.00
RADIUS   Ub1    H20 1.00
RADIUS   Ub1    H20 1.00
RADIUS   Ub1    H21 1.00
RADIUS   Ub1    H21 1.00
RADIUS   Ub1    H22 1.00
RADIUS   Ub1    H22 1.00
RADIUS   Ub1    H23 1.00
RADIUS   Ub1    H25 1.00
RADIUS   Ub1    H25 1.00
RADIUS   Ub1    H25 1.00
RADIUS   Ub1    H26 1.00
RADIUS   Ub1    H26 1.00
RADIUS   Ub1    H27 1.00
RADIUS   Ub1    H27 1.00
RADIUS   Ub1    H28 1.00
RADIUS   Ub1    H30 1.00
RADIUS   Ub1    H30 1.00
RADIUS   Ub1    H30 1.00
RADIUS   Ub1    H31 1.00
RADIUS   Ub1    H31 1.00 
RADIUS   Ub1    H32 1.00
RADIUS   Ub1    H32 1.00
RADIUS   Ub1    H33 1.00
RADIUS   Ub1    H35 1.00
RADIUS   Ub1    H35 1.00
RADIUS   Ub1    H35 1.00
RADIUS   Ub1    H36 1.00
RADIUS   Ub1    H36 1.00
RADIUS   Ub1    H36 1.00

RADIUS   Ub1    C1  1.70
RADIUS   Ub1    C2  1.70
RADIUS   Ub1    C3  1.70
RADIUS   Ub1    C4  1.70
RADIUS   Ub1    C5  1.70
RADIUS   Ub1    C6  1.70
RADIUS   Ub1    C1M 1.70
RADIUS   Ub1    C3M 1.70
RADIUS   Ub1    C4M 1.70
RADIUS   Ub1    C7  1.70
RADIUS   Ub1   1H1M 1.00
RADIUS   Ub1   2H1M 1.00
RADIUS   Ub1   3H1M 1.00
RADIUS   Ub1   1H3M 1.00
RADIUS   Ub1   2H3M 1.00
RADIUS   Ub1   3H3M 1.00
RADIUS   Ub1   1H4M 1.00
RADIUS   Ub1   2H4M 1.00
RADIUS   Ub1   3H4M 1.00
RADIUS   Ub1   1H7  1.00 
RADIUS   Ub1   2H7  1.00
RADIUS   Ub1    O2  1.40
RADIUS   Ub1    O3  1.40
RADIUS   Ub1    O4  1.40
RADIUS   Ub1    O5  1.40
RADIUS   Ub1    HO2 1.00
RADIUS   Ub1    HO5 1.00


#23456789A123456789B123456789C
#BAK

# Backbone
CHARGE   Ub1BK  C8   0.00
CHARGE   Ub1BK  C9   0.00
CHARGE   Ub1BK  C10  0.00
CHARGE   Ub1BK  C11  0.00
CHARGE   Ub1BK  C12  0.00
CHARGE   Ub1BK  C13  0.00
CHARGE   Ub1BK  C14  0.00
CHARGE   Ub1BK  C15  0.00
CHARGE   Ub1BK  C16  0.00
CHARGE   Ub1BK  C17  0.00
CHARGE   Ub1BK  C18  0.00
CHARGE   Ub1BK  C19  0.00
CHARGE   Ub1BK  C20  0.00
CHARGE   Ub1BK  C21  0.00
CHARGE   Ub1BK  C22  0.00
CHARGE   Ub1BK  C23  0.00
CHARGE   Ub1BK  C24  0.00
CHARGE   Ub1BK  C25  0.00
CHARGE   Ub1BK  C26  0.00
CHARGE   Ub1BK  C27  0.00
CHARGE   Ub1BK  C28  0.00
CHARGE   Ub1BK  C29  0.00
CHARGE   Ub1BK  C30  0.00
CHARGE   Ub1BK  C31  0.00
CHARGE   Ub1BK  C32  0.00
CHARGE   Ub1BK  C33  0.00
CHARGE   Ub1BK  C34  0.00
CHARGE   Ub1BK  C35  0.00
CHARGE   Ub1BK  C36  0.00
CHARGE   Ub1BK  H8   0.00
CHARGE   Ub1BK  H10  0.00
CHARGE   Ub1BK  H10  0.00
CHARGE   Ub1BK  H10  0.00
CHARGE   Ub1BK  H11  0.00
CHARGE   Ub1BK  H11  0.00
CHARGE   Ub1BK  H12  0.00
CHARGE   Ub1BK  H12  0.00
CHARGE   Ub1BK  H13  0.00
CHARGE   Ub1BK  H15  0.00
CHARGE   Ub1BK  H15  0.00
CHARGE   Ub1BK  H15  0.00
CHARGE   Ub1BK  H16  0.00
CHARGE   Ub1BK  H16  0.00
CHARGE   Ub1BK  H17  0.00
CHARGE   Ub1BK  H17  0.00
CHARGE   Ub1BK  H18  0.00
CHARGE   Ub1BK  H20  0.00
CHARGE   Ub1BK  H20  0.00
CHARGE   Ub1BK  H20  0.00
CHARGE   Ub1BK  H21  0.00
CHARGE   Ub1BK  H21  0.00
CHARGE   Ub1BK  H22  0.00
CHARGE   Ub1BK  H22  0.00
CHARGE   Ub1BK  H23  0.00
CHARGE   Ub1BK  H25  0.00
CHARGE   Ub1BK  H25  0.00
CHARGE   Ub1BK  H25  0.00
CHARGE   Ub1BK  H26  0.00
CHARGE   Ub1BK  H26  0.00
CHARGE   Ub1BK  H27  0.00
CHARGE   Ub1BK  H27  0.00
CHARGE   Ub1BK  H28  0.00
CHARGE   Ub1BK  H30  0.00
CHARGE   Ub1BK  H30  0.00
CHARGE   Ub1BK  H30  0.00
CHARGE   Ub1BK  H31  0.00
CHARGE   Ub1BK  H31  0.00 
CHARGE   Ub1BK  H32  0.00
CHARGE   Ub1BK  H32  0.00
CHARGE   Ub1BK  H33  0.00
CHARGE   Ub1BK  H35  0.00
CHARGE   Ub1BK  H35  0.00
CHARGE   Ub1BK  H35  0.00
CHARGE   Ub1BK  H36  0.00
CHARGE   Ub1BK  H36  0.00
CHARGE   Ub1BK  H36  0.00

#Ub101
CHARGE   Ub101  C1   0.15
CHARGE   Ub101  C2   0.38
CHARGE   Ub101  C3   0.26
CHARGE   Ub101  C4  -0.15
CHARGE   Ub101  C5   0.65
CHARGE   Ub101  C6  -0.42
CHARGE   Ub101  C1M -0.30
CHARGE   Ub101 1H1M  0.12
CHARGE   Ub101 2H1M  0.11
CHARGE   Ub101 3H1M  0.11
CHARGE   Ub101  C3M  0.12
CHARGE   Ub101 1H3M  0.03
CHARGE   Ub101 2H3M  0.03
CHARGE   Ub101 3H3M  0.03
CHARGE   Ub101  C4M -0.03
CHARGE   Ub101 1H4M  0.04
CHARGE   Ub101 2H4M  0.04
CHARGE   Ub101 3H4M  0.04
CHARGE   Ub101  C7   0.29
CHARGE   Ub101 1H7   0.01
CHARGE   Ub101 2H7   0.01
CHARGE   Ub101  O2  -0.45
CHARGE   Ub101  O3  -0.33
CHARGE   Ub101  O4  -0.27
CHARGE   Ub101  O5  -0.47

#Ub1-1
CHARGE   Ub1-1  C1  -0.04
CHARGE   Ub1-1  C2   0.25
CHARGE   Ub1-1  C3   0.10
CHARGE   Ub1-1  C4  -0.15
CHARGE   Ub1-1  C5   0.50
CHARGE   Ub1-1  C6  -0.46
CHARGE   Ub1-1  C1M -0.01
CHARGE   Ub1-1 1H1M  0.01
CHARGE   Ub1-1 2H1M  0.01
CHARGE   Ub1-1 3H1M  0.01
CHARGE   Ub1-1  C3M  0.04
CHARGE   Ub1-1 1H3M  0.06
CHARGE   Ub1-1 2H3M  0.03
CHARGE   Ub1-1 3H3M  0.03
CHARGE   Ub1-1  C4M  0.12
CHARGE   Ub1-1 1H4M  0.02
CHARGE   Ub1-1 2H4M  0.04
CHARGE   Ub1-1 3H4M  0.00
CHARGE   Ub1-1  C7   0.38
CHARGE   Ub1-1 1H7  -0.06
CHARGE   Ub1-1 2H7  -0.06
CHARGE   Ub1-1  O2  -0.57
CHARGE   Ub1-1  O3  -0.33
CHARGE   Ub1-1  O4  -0.30
CHARGE   Ub1-1  O5  -0.62

#Ub1H2
CHARGE   Ub1H2  C1   0.14
CHARGE   Ub1H2  C2   0.10
CHARGE   Ub1H2  C3   0.09
CHARGE   Ub1H2  C4  -0.02
CHARGE   Ub1H2  C5   0.26
CHARGE   Ub1H2  C6  -0.35
CHARGE   Ub1H2  C1M -0.25
CHARGE   Ub1H2  C3M  0.05
CHARGE   Ub1H2  C4M  0.15
CHARGE   Ub1H2  C7   0.39
CHARGE   Ub1H2 1H1M  0.07
CHARGE   Ub1H2 2H1M  0.07
CHARGE   Ub1H2 3H1M  0.09
CHARGE   Ub1H2 1H3M  0.05
CHARGE   Ub1H2 2H3M  0.05
CHARGE   Ub1H2 3H3M  0.05
CHARGE   Ub1H2 1H4M  0.02
CHARGE   Ub1H2 2H4M  0.02
CHARGE   Ub1H2 3H4M  0.02
CHARGE   Ub1H2 1H7  -0.05
CHARGE   Ub1H2 2H7  -0.05
CHARGE   Ub1H2  O3  -0.30
CHARGE   Ub1H2  O4  -0.34
CHARGE   Ub1H2  O2  -0.54
CHARGE   Ub1H2  O5  -0.54
CHARGE   Ub1H2  HO2  0.41
CHARGE   Ub1H2  HO5  0.41


#CHARGE   Ub1H2 1H10  0.07

TORSION  Ub1BK 1H10  C10  C9   C8   f        0.0         3      0.00
TORSION  Ub1BK 1H15  C15  C14  C13  f        0.0         3      0.00
TORSION  Ub1BK 1H20  C20  C19  C18  f        0.0         3      0.00
TORSION  Ub1BK 1H25  C25  C24  C23  f        0.0         3      0.00
TORSION  Ub1BK 1H30  C30  C29  C28  f        0.0         3      0.00
TORSION  Ub1BK 1H35  C35  C34  C33  f        0.0         3      0.00
TORSION  Ub1BK 1H36  C36  C34  C33  f        0.0         3      0.00
#TORSION  Ub101 1H1M  C1M  C1   C2   f        0.0         3      0.00
#TORSION  Ub101 1H3M  C3M  C3   C2   f        0.0         3      0.00
#TORSION  Ub101 1H4M  C4M  C4   C3   f        0.0         3      0.00
#TORSION  Ub101 1H7   C7   C6   C5   f        0.0         3      0.00
TORSION  Ub1H2 1H1M  C1M  C1   C2   f        0.0         3      0.00
TORSION  Ub1H2 1H3M  C3M  C3   C2   f        0.0         3      0.00
TORSION  Ub1H2 1H4M  C4M  C4   C3   f        0.0         3      0.00
TORSION  Ub1H2 1H7   C7   C6   C5   f        0.0         3      0.00
TORSION  Ub1H2  HO2  O2   C2   C1   f        0.0         2    180.00
TORSION  Ub1H2  HO5  O5   C5   C4   f        0.0         2    180.00
TORSION  Ub1-1 1H1M  C1M  C1   C2   f        0.0         3      0.00
TORSION  Ub1-1 1H3M  C3M  C3   C2   f        0.0         3      0.00
TORSION  Ub1-1 1H4M  C4M  C4   C3   f        0.0         3      0.00
TORSION  Ub1-1 1H7   C7   C6   C5   f        0.0         3      0.00

